--- configure.ori	2015-11-24 20:56:46.000000000 +0100
+++ configure	2015-11-24 20:59:58.000000000 +0100
@@ -253,17 +253,16 @@
   close INVERS;
 }
 else {
-  print "\nYour RepeatMasker installation is missing a library file.\n"
+  die "\nYour RepeatMasker installation is missing a library file.\n"
       . "RepeatMasker requires a minimal set of library sequences to run\n"
       . "properly.  Please check that all files were extracted from the\n"
       . "distribution before re-running the configure program.\n\n";
-  exit;
 }
 
 print "\n  -- Building monolithic RM database...";
 system(
 "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null"
-);
+) and die "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!";
 
 ##
 ## TRF location
@@ -475,7 +474,7 @@
     }
     close IN;
     close OUT;
-    system( "mv $configFile.tmp $configFile" );
+    system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
   }
 
 }
@@ -607,15 +606,15 @@
   }
   close IN;
   close OUT;
-  system( "mv $configFile.tmp $configFile" );
+  system( "mv $configFile.tmp $configFile" ) and die "Faled to mv $configFile.tmp $configFile: $!";
 
   # Freeze RM and RMPep libraries for RepeatModeler use among others
   my $rmLocation = "$FindBin::Bin";
   print "Building RMBlast frozen libraries..\n";
   system(   "$pgLocation/makeblastdb -dbtype nucl -in "
-          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype nucl -in $rmLocation/Libraries/RepeatMasker.lib failed: $!";
   system(   "$pgLocation/makeblastdb -dbtype prot -in "
-          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
 
   my $pgDefault = &promptScreen(
     "",
@@ -682,15 +681,15 @@
   }
   close IN;
   close OUT;
-  system( "mv $configFile.tmp $configFile" );
+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
 
   # Freeze RM and RMPep libraries
   my $rmLocation = "$FindBin::Bin";
   print "Building WUBlast/ABBlast frozen libraries..\n";
   system(   "$wuLocation/xdformat -n -I "
-          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed with: $!";
   system(   "$wuLocation/xdformat -p -I "
-          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
 
   my $wuDefault = &promptScreen(
     "",
@@ -756,7 +755,7 @@
       }
     }
     else {
-      print "ERROR: Could not find nhmmer program in this directory!\n";
+      print "ERROR: Could not find nhmmer program in '$location' directory!\n";
     }
   }
 
@@ -776,7 +775,7 @@
   }
   close IN;
   close OUT;
-  system( "mv $configFile.tmp $configFile" );
+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
 
   my $default = &promptScreen(
     "",
@@ -830,7 +829,7 @@
   }
   close IN;
   close OUT;
-  system( "mv $configFile.tmp $configFile" );
+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
 
   my $deDefault = &promptScreen(
     "",
@@ -866,9 +865,6 @@
 
   my $answer = undef;
 
-  # Clear the screen
-  system( "clear" );
-
   print "\n\n\n";
   print $screenText;
   my $numLines = ( $screenText =~ s/(\n)/$1/g );